Sunday, 18 January 2015

Big changes for the Victorian Bioinformatics Consortium


I have spent all 12 years of my postdoc life at the Victorian Bioinformatics Consortium (VBC) based at Monash University in Melbourne, Australia. The VBC was started by Professor Ross Coppel way back in 2002, a leader I greatly respect and thank for his vision and support of bioinformatics in Australia. Ross remains the director of the VBC to this day.

I began as a junior researcher at the VBC during the early well funded years (pre-NGS), and then as a senior researcher in the middle lean but productive years (NGS took off), and finally as scientific director during the last few years where I negotiated the VBC to become the Monash node of the greater Victorian Life Sciences Computation Initiative (VLSCI). The VLSCI was a joint initiative between the three biggest universities in Victoria, and it enabled us to triple in size to 6 bioinformaticians by funding 65% of our salaries. This enabled us to build a critical mass of staff with complementary expertise.

What's happened?

Unfortunately, the original VLSCI agreement ended on 31 Dec 2014, and Monash University declined to participate in the second round for various strategic and political reasons, despite all our attempts to persuade the Office of the Provost. This means the VBC is no longer eligible for VLSCI funding, so we can no longer operate as previously. The university has decided to start a separate dedicated bioinformatics core unit called the Monash Bioinformatics Platform (MBP).

I hoped the MBP could co-exist with the VBC/VLSCI but there were some incompatibilities. Understandably, the MBP will be service focussed and hence restricted to working on Monash-based projects only, and has little scope for bioinformatics research and tool development. The initial budget of the MBP was also insufficient to employ all existing VBC staff.

My strongest collaborations are with A/Prof Tim Stinear and Prof Ben Howden, both of whom were originally at Monash but now work at the University of Melbourne, and I have 4 NHMRC grants and an ARC LIEF grant with them. I want to work in microbial genomics which is only a minor interest to the MBP, and the Monash Department of Microbiology at Monash has no capacity or interest in employing me directly. The logical decision is to move.

What did you decide?

I have left Monash University. Yes, really! I started at Monash in 1992 as an undergraduate student, so that's 22 years or just shy of half of my life. I have accepted a position as Lead Bioinformatician at the VLSCI, including a promotion to Associate Professor. This is not a permanent or tenured position, but I did double my previous best contract length from 1 year to 2 years. I will remain an adjunct in the Department of Microbiology at Monash University, where I share an ARC grant with A/Prof John Boyce.

What will you be working on?

My primary research role will be leading the Microbial/Non-Model Genomics theme of the VLSCI (the other themes are Cancer Genomics and Clinicogenomics). I will get to once again work closely with Tim Stinear and Ben Howden, and continue developing tools for microbial genomics analysis. One of my main goals is transitioning the Melbourne Diagnostic Unit Public Health Laboratory (MDU) to a whole-genome sequencing and bioinformatics workflow, and then rolling this out to public health microbiology labs nationally. This new role will allow me to dedicate more time to the tools and methods that I think give most value back to the scientific community.

What about everyone else?

  • Dieter Bulach has moved to the VLSCI, where he will working closely with me in MDU and Microbiology working on genomics projects.
  • Simon Gladman has also moved to the VLSCI and is continuing his work with the Dental School and the Genomics Virtual Laboratory (GVL).
  • David Powell has taken a promotion and will head the new Monash Bioinformatics Platform (MBP).
  • Paul Harrison has taken a position with the MBP at Monash, and will continue to work with Traude Beilharz.
  • Fernando Rossello has stayed at Monash but joined the lab of Jose Polo in the Australian Regenerative Medicine Institute.
  • Ross Coppel remains at Monash where he is the Deputy Dean and Dean of Research in the Faculty of Medicine.

Where will you be located?

I will regularly be at VLSCI headquarters, but I will spend most of my time at the new Doherty Institute for Infection and Immunity on Level 1 in the Microbial Diagnostic Unit (MDU). I share an office with Dieter Bulach, and we have a window view overlooking Grattan St where I can see trees and natural light!

What about the VBC web presence?

The VBC website will be revamped to explain the situation and direct people appropriately. Legacy URLs, especially those published ones, will be redirected as needed. The group GitHub repositories will slowly be migrated to personal repositories. All of us except Simon will still have our email addresses. The web services available on will remain for the time being, but eventually that server will be decommissioned, with some services being terminated and some being migrated to a new location.

Closing thoughts

I am sad that the VBC had to end so soon after gaining new momentum. The VBC team was a close-knit family, and I will miss working with Fernando and Paul, and especially David Powell who I've known for 27 years and respect immensely. Monash is very fortunate to have retained him because his leadership, planning and technical abilities will be essential to making the new MBP thrive.

I've slowly worked through the stages of grief and am now enthusiastic about starting a new era in the Parkville precinct which is the biggest biomedical research hub in Australia. I expect to have more time to work on tools for microbial genomics, and maybe even finally write the papers for some of them! I have a new amazing PhD student Jason Kwong, and a great bunch of colleagues at the VLSCI. I will continue to have a role in the Australian bioinformatics community, including supporting the new Australian Bioinformatics and Computational Biology Society and the Australian Bioinformatics Conference.

My final thanks go to my former boss, Prof Ross Coppel, who was ahead of his time at Monash in starting the VBC, and who took a chance on a young computer science PhD graduate who had never studied biology before, and supported him over many years because he believed in bioinformatics being a critical area of expertise Australia needed.